The traditional realm of comparative physiologists is the phenotype. Researchers in this field are generally interested in how organisms work at the organ system, organ, tissue, cellular, organellar and protein levels of organisation. They are fascinated by the wide range of environmental conditions in which organisms exist and how this is matched by the type and capacity of the physiological mechanisms that they employ. In the post-genomic era, the molecular toolbox of several model species is available in the form of fully sequenced genomes and it can be argued that a true integrative view of how organisms function is incomplete without linking genotypes to the encoded phenotypes in the form of proteins, organelles, cells, etc. A major challenge for experimental biologists in the postgenomic era is therefore trying to close the so-called phenotype-genotype gap.Given the complexity of even a single cell and the emergence of new, unpredictable features at each of the higher levels of biological organisation, it is very difficult, if not impossible, to predict the working of complex physiological systems solely from the underlying genotype. Closure of the phenotype-genotype gap therefore appears a daunting task. Biology, however, unlike physics, can be seen as having already found its single unifying concept, or grand formula: namely evolutionary theory. Thus, looking for the ultimate/evolutionary cause of a physiological mechanism in addition to the proximate/mechanistic cause should help to understand the distribution of particular physiological phenotypes and their associated genotypes in organisms. Thus, the fundamental question for comparative physiologists can be broadened from 'How does it work? ' (Schmidt-Nielsen, 1997a) to 'How did it come about to work like it does? ' (Sherwood et al., 2005a).This review uses the mechanism of oxygen secretion in fishes, which has been intensively studied in the fish swimbladder for over 100·years, to demonstrate the potential insights from such an evolutionary approach. The long generation times of the study species preclude the use of The ability of some fishes to inflate their compressible swimbladder with almost pure oxygen to maintain neutral buoyancy, even against the high hydrostatic pressure several thousand metres below the water surface, has fascinated physiologists for more than 200·years. This review shows how evolutionary reconstruction of the components of such a complex physiological system on a phylogenetic tree can generate new and important insights into the origin of complex phenotypes that are difficult to obtain with a purely mechanistic approach alone. Thus, it is shown that oxygen secretion first evolved in the eyes of fishes, presumably for improved oxygen supply to an avascular, metabolically active retina. Evolution of this system was facilitated by prior changes in the pH dependence of oxygen-binding characteristics of haemoglobin (the Root effect) and in the specific buffer value of haemoglobin. These changes predisposed teleost fishes for the...